A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

• Published in: Nature (London) 2010-12, Vol.468 (7325), p.815-818
• Main Authors: Domazet-Lošo, Tomislav, Tautz, Diethard
• Format: Article
• Language: English
• Subjects: 631/136; 631/181/757; Aging; Aging - genetics; Animals; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Conserved Sequence; Evolutionary biology; Female; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genetic aspects; Genetics of eukaryotes. Biological and molecular evolution; Genomics; Humanities and Social Sciences; letter; Male; Models, Biological; multidisciplinary; Oligonucleotide Array Sequence Analysis; Phylogeny; Physiological aspects; RNA; Science; Science (multidisciplinary); Sex Characteristics; Vertebrata; Zebrafish - classification; Zebrafish - embryology; Zebrafish - genetics; Zebrafish - growth & development
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature09632

Parallels between phylogeny and ontogeny have been discussed for almost two centuries, and a number of theories have been proposed to explain such patterns. Especially elusive is the phylotypic stage, a phase during development where species within a phylum are particularly similar to each other. Although this has formerly been interpreted as a recapitulation of phylogeny, it is now thought to reflect an ontogenetic progression phase, where strong constraints on developmental regulation and gene interactions exist. Several studies have shown that genes expressed during this stage evolve at a slower rate, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage. Here we use a combination of phylostratigraphy and stage-specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Notably, ageing animals express increasingly older genes. Comparisons with similar data sets from flies and nematodes show that this pattern occurs across phyla. Our results indicate that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.